PSICS Results for run-onset.xml

step-onset (run-onset.xml)

Voltage clamp step onset behavior for continuous and stochastic channels. The step begins at 1.985ms and the timestep is 0.02ms. This uses the midpoint evaluation method for the step, (stepStyle = midpoint in the voltage clamp) so the effect is as if the step started at 1.980ms. This fugure should be compared with the file run-onset-avg, which does the same calculation but with stepStyle = average for the clamp.

Total CPU time 0.2210 seconds; at 16:38:53 Fri 28 Sep 2007

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	time/ms	timestep/ms	stochThreshold	CPU Time / s
1	0 / 0	201 / 1	16.0	0.02	0	0.1
1	201 / 1	0 / 0	16.0	0.02	1000	0.121

Predefined views

whole

start

All files

Model	Preprocessed	Outupt data	Reference data etc
run-onset.xml cell.xml membrane.xml environment.xml recording-short.xml na1.xml summary.xml view.xml recording-short-avg.xml	out-16-fdata.txt out-0-fdata.txt out-1000-fdata.txt	out-16-f.dat out-16-f.txt out-0-f.dat out-0-f.txt out-1000-f.dat out-1000-f.txt	step-onset.jar

Model

Archive file of the complete model: step-onset.jar

run-onset.xml

<PSICSRun timeStep="0.02ms" runTime="16ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording-short"
	stochThreshold="0"
	repeats="20">
	<StructureDiscretization baseElementSize="3um"/>

<RunSet vary="stochThreshold" values="[0, 1000]"
                filepattern="out-$.txt">
	</RunSet>



<About>
Voltage clamp step onset behavior for continuous and stochastic channels. The step begins
at 1.985ms and the timestep is 0.02ms. This uses the midpoint evaluation method for the step,
(stepStyle="midpoint" in the voltage clamp)
so the effect is as if the step started at 1.980ms. This fugure should be compared with
the file run-onset-avg, which does the same calculation but with stepStyle="average" for the clamp.
 </About>



	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>

		<LineSet file="out-1000-f.txt" color="red" maxshow="6"/>
		<LineSet file="out-0-f.txt" color="green" maxshow="2"/>

		 <View id="whole" xmin="0." xmax="20." ymin="-360." ymax="30."/>
		 <View id="start" xmin="1.93" xmax="2.15" ymin="-260." ymax="30."/>
		</LineGraph>


	</ViewConfig>


</PSICSRun>

cell.xml

<CellMorphology id="cell">

    <Point id="p0" x="0" y="0" z="0" r="1."/>

</CellMorphology>

membrane.xml

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">

	<ChannelPopulation id="napop" channel="na1" density="16per_um2"/>


</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="80mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

recording-short.xml

<Access id="recording-short" saveInterval="0.05ms">

	<VoltageClamp at="p0" lineColor="red" hold="-80.0mV" stepValue="midpoint">
		<VoltagePulse id="vstep" start="1.985ms" to="30mV"
			      duration="10ms"/>
	</VoltageClamp>

</Access>

na1.xml

<KSChannel id="na1" gSingle="30pS" permeantIon="Na">
	<ClosedState id="c1"/>
	<OpenState id="o1"/>
	<ClosedState id="c2"/>

	<VHalfTransition from="c1" to="o1" vHalf = "-35mV" z="4.5e" gamma="0.8" tau="0.55ms" tauMin="0.1ms"/>

	<VHalfTransition from="o1" to="c2" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="12.0ms" tauMin="1.5ms"/>

</KSChannel>

recording-short-avg.xml

<Access id="recording-short" saveInterval="0.05ms">

	<VoltageClamp at="p0" lineColor="red" hold="-80.0mV" stepValue="average">
		<VoltagePulse id="vstep" start="1.985ms" to="30mV"
			      duration="10ms"/>
	</VoltageClamp>

</Access>